SMTL ID : 4h2e.2 (1 other biounit)

Crystal structure of an MMP twin inhibitor complexing two MMP-9 catalytic domains

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.90 Å

Oligo State

monomer

Ligands

2 x ZN: ZINC ION(Non-covalent)

ZN.1: 4 residues within 4Å: Chain A: H.121, H.125, H.131 Ligands: 0Y3.6 3 PLIP interactions: 3 interactions with chain A Metal complexes: A:H.121, A:H.125, A:H.131 ZN.2: 4 residues within 4Å: Chain A: H.70, D.72, H.85, H.98 5 PLIP interactions: 5 interactions with chain A Metal complexes: A:H.70, A:D.72, A:D.72, A:H.85, A:H.98

3 x CA: CALCIUM ION(Non-covalent)

CA.3: 5 residues within 4Å: Chain A: A.59, D.60, G.92, Q.94, D.96 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:D.60, A:G.92, A:Q.94, A:D.96 CA.4: 6 residues within 4Å: Chain A: D.77, G.78, D.80, L.82, D.100, E.103 5 PLIP interactions: 5 interactions with chain A Metal complexes: A:G.78, A:D.80, A:L.82, A:D.100, A:E.103 CA.5: 5 residues within 4Å: Chain A: S.24, D.26, D.101, E.103, W.105 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:D.26, A:D.101, A:D.101, A:E.103

1 x 0Y3: N,N'-bis(4-{[(3R)-3-[(biphenyl-4-ylsulfonyl)(propan-2-yloxy)amino]-4-(hydroxyamino)-4-oxobutyl]amino}-4-oxobutyl)benzene-1,3-dicarboxamide(Non-covalent)

0Y3.6: 21 residues within 4Å: Chain A: G.1, F.2, G.81, L.82, L.83, A.84, H.85, L.117, V.118, H.121, E.122, H.125, D.130, H.131, S.133, L.138, Y.140, P.141, M.142, Y.143 Ligands: ZN.1 16 PLIP interactions: 16 interactions with chain A Hydrophobic interactions: A:F.2, A:L.82, A:L.83, A:V.118, A:H.121, A:H.131, A:L.138, A:Y.140, A:P.141, A:M.142, A:Y.143, A:Y.143 Hydrogen bonds: A:A.84, A:A.84, A:D.130 Salt bridges: A:E.122

3 x PEG: DI(HYDROXYETHYL)ETHER(Non-functional Binders)

PEG.7: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP) PEG.8: 3 residues within 4Å: Chain A: G.73, P.75 Ligands: PEG.9 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:G.73 PEG.9: 4 residues within 4Å: Chain A: D.72, G.73, Y.74 Ligands: PEG.8 No protein-ligand interaction detected (PLIP)

1 x ACT: ACETATE ION(Non-functional Binders)

ACT.10: 4 residues within 4Å: Chain A: K.109, F.145, T.146, E.147 1 PLIP interactions: 1 interactions with chain A Hydrophobic interactions: A:F.145

1 x BCN: BICINE(Non-covalent)

BCN.11: 4 residues within 4Å: Chain A: A.68, E.69, P.75, F.76 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:F.76 Salt bridges: A:E.69

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Antoni, C. et al., Crystallization of bi-functional ligand protein complexes. J.Struct.Biol. (2013)

Release Date

2013-04-24

Peptides

Matrix metalloproteinase-9: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
B

Matrix metalloproteinase-9

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